On Thu, Apr 11, 2013 at 6:17 AM, manara r. (rm16g09) <rm16...@soton.ac.uk>wrote:
> Dear gmx-users, > > I am having a problem with a periodic molecule and the domain > decomposition, I wish to use a high number of processors (circa 180, but > can obviously be reduced) and therefore need to use the -rdd or -dds flags > (I believe), how do these value effect the simulation? > > The box size is 11.5 x 11.5 x 45. > > The polymer contains charged groups every repeating unit. > > The error I'm getting is (note this is a test run on my home machine, not > the cluster): > Fatal error: > There is no domain decomposition for 4 nodes that is compatible with the > given box and a minimum cell size of 61.7923 nm > Change the number of nodes or mdrun option -rdd or -dds > > There is no amount of hacking of -rdd or -dds that will "solve" this problem. DD cell size should be on the order of the longest cutoff. Your minimum size is huge, indicating you probably have either a bad topology or incorrect .mdp settings. http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
